title: 09-7 [ssBCR-Seq]

status: Public on Aug 20 2023

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Library strategy: scBCR-seq
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Quality control was performed removing sequences with nonproductive arrangements, lacking valid V or J gene annotation. Cells were further filtered that have exactly one heavy chain sequence.
B cell clones were inferred based on heavy chain sequences using hierarchical clustering with single-linkage (Gupta 2017) for each subject with day 0 and day 7 cells combined. Sequences were first partitioned based on common V and J gene annotations and junction lengths. Within each partition, sequences whose junction sequences were within 0.12 normalized Hamming distances between each other were clustered as clones. The cutoff was chosen based on manual inspection of the bimodal distance-to-nearest distribution.
Somatic hypermutation frequency was computed using the “calcObservedMutations” function from SHazaM v1.0.2 package (Gupta 2015) and was the number of nucleotide mismatches from the germline sequences of the heavy chain variable segments leading up to the CDR3.
Genome_build: GRCh38
Supplementary_files_format_and_content: BCR-seq results were saved in AIRR-tsv format and gzip compressed.
Supplementary_files_format_and_content: Tar archives include cell ranger output files.

source_name: single-cell BCR-seq of human: adult female PBMC seven days post vaccination

extract_protocol:
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 150x150 paired-end reads was used to sequence gene expression libraries.

value: seven days post vaccination

value: PBMC

value: B-cell

value: female

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: White

tag: library type

value: scBCR-seq


title: 15-0 [ssBCR-Seq]

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: single-cell BCR-seq of human: adult male PBMC pre-vaccination

tag: timepoint

value: pre-vaccination

tag: tissue

tag: cell type

tag: Sex

value: male

tag: age

value: Hispanic or Latino


title: 09-0 [ssBCR-Seq]

source_name: single-cell BCR-seq of human: adult female PBMC pre-vaccination


title: 15-7 [ssBCR-Seq]

source_name: single-cell BCR-seq of human: adult male PBMC seven days post vaccination


title: D21 V IFN rep3

status: Public on Sep 12 2023

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

description: RNA-seq from euploid lymphoblastoid cells

data_processing:
Read trimming using bbduk (options: ktrim=r qtrim=r1, trimq=10, k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2
Reads over hg38 refseq gene annotations were counted using featurecounts and then RPKM normalized. Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Normalization of samples based on size factors and statistical analysis of comparisons between experimental condtions were performed using DESEQ2; for intergenotype (T21 vs D21) comparisons, expression of genes on chromosome 21 was normalized to account for ploidy
Tdfs were generated from trimmed BAM files using igvtools
Splicing analysis was performed with rMATS (4.0.1) and sashimi plots were generated from rMATs result using a modified script based on ggsashimi.py
Assembly: hg38
Supplementary files format and content: csv file with log2fold change and adj p-value for each gene for each comparison, both within-genotype (looking at treatmetn effects) and between-genotype (looking at basal differences in T21 vs D21 or differential effects of treatment)

source_name: Euploid immortalized lymphoblastoid

growth_protocol: Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine

extract_protocol:
4 hours after vehicle or IFNγ treatment, cells were collected, spun down, washed once in PBS, then resuspended in TRIzol reagent (Invitrogen, 15596026) and snap frozen. After all 3 biological replicates were collected, cell lysates in TRIzol were thawed and total RNA was extracted according to the manufacturer's protocol. RNA concentration was measured by Qubit and quality was verified using a TapeStation
Protocol for Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan, 0520) was used
Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan, 0520)

treatment_protocol: Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask. After 30 minutes, media containing either vehicle (final concentration 40 μM Tris pH 7.4) or 10 ng/mL recombinant IFNγ (Gibco, PHC4031)

tag: cell line

value: Euploid immortalized lymphoblastoid

value: immortalized lymphoblastoid

tag: treatment

value: 0.01% DMSO + 10 ng/mL IFNγ

tag: treatment delivery method

value: Treatment diluted in media and added to flasks with cells

tag: molecule type

value: Small molecule + cytokine


title: 94-7 [ssBCR-Seq]


title: 94-0 [ssBCR-Seq]


title: 67-0 [ssBCR-Seq]


title: 67-7 [ssBCR-Seq]


title: 15-0 [ssRNA-Seq]

library_source: transcriptomic single cell

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Gene expression analysis of CellRanger output was performed using Seurat v.3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv & features.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: single-cell RNA-seq of human: adult male PBMC pre-vaccination

extract_protocol:
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 100x100 paired-end reads was used to sequence gene expression libraries.
ssRNA-Seq

value: scRNA-seq


title: 48-0 [ssBCR-Seq]


title: 48-7 [ssBCR-Seq]


title: 15-7 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult male PBMC seven days post vaccination


title: 09-0 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult female PBMC pre-vaccination


title: Cpt2164

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
R30C2_AlbCrevsCpt2_AlbCre_deg.txt
Cpt2_AlbCrevsRab30Cpt2_f_deg.txt

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Downstream analysis using the DESeq2 package in R was performed independently by the investigators to normalize raw read counts for comparisons across all samples.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: TotalNormCounts041123v2.txt includes the downstream DESeq2 analysis (with Wald test, betaPrior=FALSE, and genes with at least 1 count) performed by the investigators with normalized read counts and the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Rab30_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Rab30 liver-specific KO samples to Rab30;Cpt2 floxed control (littermates to DKO) samples. Tab-delimited text file.
Supplementary files format and content: Rab30KOvsRab30WT_deg.txt includes the differential analysis results of all genes when comparing Rab30 whole-body KO to WT littermates to Rab30 whole-body KO. Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsCpt2_AlbCre_deg.txt includes the differential analysis results of all genes when comparing Rab30;Cpt2 liver-specific DKO to Cpt2 liver-specific KO. Tab-delimited text file.
Supplementary files format and content: Cpt2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to Rab30;Cpt2 floxed control (littermates to DKO). Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis of all genes when comparing Rab30;Cpt2 liver-specific DKO to Rab30;Cpt2 flozed control (littermates to DKO). Tab-delimited text file.

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was extracted from flash frozen liver tissue using TRIzol reagent (Invitrogen for Thermo Fisher Scientific, 15596026) with additional purification using RNeasy Mini Kit (Qiagen, 74106), as per manufacturers’ instructions. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc (https://en.novogene.com/services/research-services/transcriptome-sequencing/).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

value: liver

tag: genotype

value: Cpt2 liver-specific KO

value: 24hr fast


title: Cpt2802


title: 94-7 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult female PBMC seven days post vaccination

value: seven days post vaccination

value: PBMC

value: B-cell


title: 93-7 [ssRNA-Seq]

value: female

value: Not Hispanic or Latino

value: White


title: Cpt2166


title: 94-0 [ssRNA-Seq]

value: pre-vaccination


title: 67-7 [ssRNA-Seq]


title: 67-0 [ssRNA-Seq]


title: 48-7 [ssRNA-Seq]

value: male


title: 48-0 [ssRNA-Seq]


title: 93-0 [ssBCR-Seq]

value: scBCR-seq


title: RNA_Sample_4_spleen_RECURRENT1

status: Public on Aug 19 2023

city: Los Angeles

first: Michelle

last: Jones

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description:
28601_1_spleen (Recurrent)
raw TPM column name: 28601_1_spleen

data_processing:
Reads within each fastq file were first trimmed using TrimGalore to remove low quality bases and sample barcodes, retaining reads 75bp or longer. Each transcriptome is then aligned to hg38 and the Gencodev29 primary assembly [41]. Genes are quantified with RSEM [43] and Kallisto [44]. Sample-specific gene models were generated using alignments produced with STAR two pass mapping and Stringtie [45]. Gene expression values were shown as normalized variance stabilizing transformation (vst) counts. To measure RNA abundance, we first obtained BAM alignment quality metrics using Picard (http://broadinstitute.github.io/picard). Samples with less than 90 percent of reads mapped to the correct strand of the reference genome (PCT_CORRECT_STRAND_READS) were omitted. Patients whose primary and recurrent tumors both passed this quality control were retained (n = 50) (Additional File1, Supplementary Table 2). Read counts were quantified using the R package Salmon [46] at transcript level and reads were mapped to Genecode Release 29 (GRCh38) comprehensive gene annotations by R package ‘tximport’ [47]. To filter out potential artifacts and very low expressed transcripts we retained transcripts with length greater than 300bp, TPM (Transcripts Per Million) value greater than 0.05 and isoform percentage greater than 1%. Transcripts in blacklist regions [48] were also filtered out. We retained transcripts expressed in more than 5 samples, which resulted in 91,411 transcripts from 33,969 genes. Tumor purity was estimated by the degree of heterogeneity of the tumor microenvironment. We applied the R package ‘consensusTME’ [49] to estimate cell type specific enrichment scores based on TCGA ovarian cancer data, and confirmed there was low stromal content and generally low infiltration by immune cells across the samples (Additional File2, Supplementary Fig.1).
Differentially expressed genes between theBRCA1/2carrier versusBRCA1/2non-carrier and primary versus recurrent tumors were detected by R package ‘DESeq2’ [50]. TheP-values were adjusted for multiple testing using the Benjamini–Hochberg procedure. Since our experiment design has group-specific effects, comparisons betweenBRCAcarrier status are made between patients, while comparisons between primary versus recurrent tumors are made within the patient. To control for confounding differences between the primary and recurrent tumors from patients we constructed a nested DEseq2 model with formula; ~ purity + BRCAStatus + BRCAStatus:PatientID + BRCAStatus:isRecur, which has the main effect for BRCA status plus nested interactions with primary and recurrent status. To see whether the identified gene sets (e.g. genes inside PMDs or differentially expressed genes) show significant functional concordance, we performed Gene Set Enrichment Analysis [51] for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [52]. We implemented enrichment analysis with R package ‘clusterProfiler’ [53]. For each enrichment analysis, we set the number of permutations to 10,000 and reported enriched pathways with a Benjamini–Hochberg adjustedP-value less than 0.05.
Assembly: hg38
Supplementary files format and content: text file containing transcript per million data obtained from Salmon package comparing samples with and without BRCA mutations
Supplementary files format and content: text file containing transcript per million data obtained from Salmon package comparing primary tumor samples vs recurrent tumor samples
Supplementary files format and content: text file with the raw TPM/abundance

source_name: ovarian cancer tumors

extract_protocol:
Fresh frozen tumors were embedded in optimal cutting temperature compound, bisected and mounted and two slides were made for hematoxylin and eosin (H&E) staining. Each punch was divided into three pieces, two of which were used for genomic DNA (gDNA) extraction using the Machery-Nagel Nucleospin DNA Kit and the third for RNA extraction using the Machery-Nagel Nucleospin RNA Kit
Sequencing libraries were prepared by adding 1ug of RNA to the TruSeq Stranded Total RNA Kit with Ribo- and Mito- depletion following the TruSeq standard protocol with 15 cycles of PCR. Libraries were quantified using Qubit RNA Broad Range kit and pooled before being run on one lane of a HiSeq2000 to collect ~ 1M reads per library for quality control. PCR duplication rate was estimated in this low coverage sequencing run in 150bp paired end mode, and library complexity was estimated using PreSeq. Based on the complexity measured in this low coverage sequencing experiment we estimated the maximal coverage that would continue to provide informative measurement of transcripts in the library was ~ 350 M reads. Each library was then pooled and this pool was sequenced in 2 × 150 bp mode on an Illumina Novaseq 6000, and we generated ~ 335 million reads from each library.

value: ovarian cancer tumors

tag: tumor source tissue

value: Spleen

tag: brca genotype

tag: tumor type

value: Recurrent


title: 93-7 [ssBCR-Seq]


title: RNA_Sample_1_colon_RECURRENT2

description:
22421_2_rectum (Recurrent)
raw TPM column name: N/A (filtered for internal QC)

value: Rectum


title: RNA_Sample_19_diaphragm_RECURRENT1

description:
25258_1_diaphragm (Recurrent)
raw TPM column name: 25258_1_diaphragm

value: Diaphragm


title: RNA_Sample_9_omentum_PRIMARY

description:
18915_0_omentum (Primary)
raw TPM column name: N/A (filtered for internal QC)

value: Omentum

value: Primary


title: RNA_Sample_6_left inguinal lymph node_RECURRENT1

description:
41245_1_l_ing_lymph_node (Recurrent)
raw TPM column name: 41245_1_l_ing_lymph_node

value: Left ing lymph node


title: RNA_Sample_10_left side wall_RECURRENT1

description:
27561_1_l_side_wall (Recurrent)
raw TPM column name: 27561_1_l_side_wall


title: RNA_Sample_7_left adenexa_PRIMARY

description:
18975_0_l_adenexa (Primary)
raw TPM column name: 18975_0_l_adenexa

value: Left adenexa


title: 09-7 [ssRNA-Seq]

value: seven days post vaccination

value: PBMC

value: scRNA-seq


title: RNA_Sample_8_right ovary_PRIMARY

description:
17687_0_r_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)

value: Ovary - Right


title: RNA_Sample_5_left ovary_PRIMARY

description:
16030_0_l_ovary (Primary)
raw TPM column name: 16030_0_l_ovary

value: Ovary - Left

value: BOTH


title: RNA_Sample_3_right ovary_PRIMARY

description:
27481_0_r_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_3_left ovary_PRIMARY

description:
27481_0_l_ovary (Primary)
raw TPM column name: 27481_0_l_ovary


title: RNA_Sample_1_omentum_PRIMARY

description:
22421_0_omentum (Primary)
raw TPM column name: 22421_0_omentum


title: RNA_Sample_11_diaphragm_PRIMARY

description:
21739_0_diaphragm (Primary)
raw TPM column name: 21739_0_diaphragm


title: RNA_Sample_19_left ovary_PRIMARY

description:
25258_0_l_ovary (Primary)
raw TPM column name: 25258_0_l_ovary


title: RNA_Sample_1_right ovary_PRIMARY

description:
22421_0_r_ovary (Primary)
raw TPM column name: 22421_0_r_ovary


title: 93-0 [ssRNA-Seq]

value: pre-vaccination

value: B-cell

value: female

value: Not Hispanic or Latino

value: White


title: RNA_Sample_2_left ovary_PRIMARY

description:
16006_0_l_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)

value: ovarian cancer tumors


title: RNA_Sample_1_rectum_RECURRENT1

description:
22421_1_rectum (Recurrent)
raw TPM column name: 22421_1_rectum

value: Rectum

value: Recurrent


title: RNA_Sample_10_omentum_PRIMARY

description:
27561_0_omentum (Primary)
raw TPM column name: 27561_0_omentum

value: Omentum

value: Primary


title: RNA_Sample_6_pelvic lymph nodes_PRIMARY

description:
41245_0_pelvic_lymph_nodes (Primary)
raw TPM column name: 41245_0_pelvic_lymph_nodes

value: Pelvic Lymph Node


title: RNA_Sample_10_pelvis_RECURRENT2

description:
27561_2_uq_pelvis (Recurrent)
raw TPM column name: 27561_2_uq_pelvis

value: Pelvis


title: RNA_Sample_11_abdominal wall_RECURRENT1

description:
21739_1_abd_wall (Recurrent)
raw TPM column name: 21739_1_abd_wall

value: Abdominal Wall


title: RNA_Sample_4_right ovary_PRIMARY

description:
28601_0_r_ovary (Primary)
raw TPM column name: 28601_0_r_ovary


title: RNA_Sample_6_right inguinal lymph node_RECURRENT1

description:
41245_1_r_ing_lymph_node (Recurrent)
raw TPM column name: 41245_1_r_ing_lymph_node

value: Right ing lymph node


title: RNA_Sample_5_pelvis_RECURRENT3

description:
16030_3_pelvis (Recurrent)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_5_pelvis_RECURRENT1

description:
16030_1_pelvis (Recurrent)
raw TPM column name: 16030_1_pelvis


title: RNA_Sample_3_pelvis_RECURRENT2

description:
27481_2_pelvis (Recurrent)
raw TPM column name: 27481_2_pelvis


title: RNA_Sample_3_diaphragm_RECURRENT3

description:
27481_3_diaphragm (Recurrent)
raw TPM column name: 27481_3_diaphragm

value: Diaphram


title: RNA_Sample_25_right ovary_PRIMARY

description:
48986_0_r_ovary (Primary)
raw TPM column name: 48986_0_r_ovary

value: Ovary - Right


title: RNA_Sample_24_right ovary_PRIMARY

description:
15815_0_r_ovary (Recurrent)
raw TPM column name: N/A (filtered for internal QC)

value: Ovary right


title: RNA_Sample_23_lymph nodes_RECURRENT2

description:
41323_2_lymph_node (Recurrent)
raw TPM column name: 41323_2_lymph_node

value: Lymph Node


title: RNA_Sample_17_omentum_PRIMARY

description:
37306_0_omentum (Primary)
raw TPM column name: 37306_0_omentum

value: TCGA A Omentum


title: RNA_Sample_15_left ovary_PRIMARY

description:
40729_0_l_ovary (Primary)
raw TPM column name: 40729_0_l_ovary


title: RNA_Sample_13_spleen_RECURRENT2

description:
32761_2_spleen (Recurrent)
raw TPM column name: 32761_2_spleen

value: Spleen


title: RNA_Sample_28_lymph nodes_RECURRENT1

description:
47573_1_lymph_node (Recurrent)
raw TPM column name: 47573_1_lymph_node


title: RNA_Sample_14_rectum_RECURRENT3

description:
30961_3_rectum (Recurrent)
raw TPM column name: 30961_3_rectum


title: RNA_Sample_23_omentum_PRIMARY

description:
41323_0_omentum (Primary)
raw TPM column name: 41323_0_omentum


title: RNA_Sample_17_brain_RECURRENT1

description:
37306_2_brain (Recurrent)
raw TPM column name: 37306_2_brain

value: Brain


title: RNA_Sample_7_small intestine_RECURRENT2

description:
18975_2_s_intestine (Recurrent)
raw TPM column name: 18975_2_s_intestine

value: Small intestine


title: RNA_Sample_21_left ovary_PRIMARY

description:
29764_0_l_ovary (Primary)
raw TPM column name: 29764_0_l_ovary

value: ovarian cancer tumors

value: Ovary - Left


title: RNA_Sample_26_right ovary_PRIMARY

description:
24892_0_r_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_14_right ovary_PRIMARY

description:
30961_0_r_ovary (Primary)
raw TPM column name: 30961_0_r_ovary


title: RNA_Sample_27_right adnexa_PRIMARY

description:
45097_0_r_adnexa (Primary)
raw TPM column name: 45097_0_r_adnexa

value: Adnexa - Right


title: RNA_Sample_26_vagina_RECURRENT1

description:
24892_1_vagina (Recurrent)
raw TPM column name: N/A (filtered for internal QC)

value: Vagina

value: Recurrent


title: RNA_Sample_27_lymph nodes_RECURRENT1

description:
45097_1_lymph_node (Recurrent)
raw TPM column name: 45097_1_lymph_node


title: RNA_Sample_22_lymph nodes_RECURRENT1

description:
24487_1_lymph_node (Recurrent)
raw TPM column name: 24487_1_lymph_node


title: RNA_Sample_15_omentum_RECURRENT1

description:
40729_2_omentum (Recurrent)
raw TPM column name: 40729_2_omentum

value: Omentum


title: RNA_Sample_28_left ovary_PRIMARY

description:
47573_0_l_ovary (Primary)
raw TPM column name: 47573_0_l_ovary

value: Primary


title: RNA_Sample_12_left ovary_PRIMARY

description:
26862_0_r_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_22_left ovary_PRIMARY

description:
24487_0_l_ovary (Primary)
raw TPM column name: 24487_0_l_ovary


title: RNA_Sample_20_lymph nodes_RECURRENT2

description:
21020_2_lymph_node (Recurrent)
raw TPM column name: 21020_2_lymph_node


title: RNA_Sample_9_spleen_RECURRENT3

description:
18915_3_spleen (Recurrent)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_20_ovary_PRIMARY

description:
21020_0_ovary (Primary)
raw TPM column name: 21020_0_ovary

value: Ovary


title: RNA_Sample_25_abdomen_RECURRENT1

description:
48986_1_abd_wall (Recurrent)
raw TPM column name: 48986_1_abd_wall

value: Abdominal


title: RNA_Sample_18_spleen_RECURRENT1

description:
19155_2_spleen (Recurrent)
raw TPM column name: N/A (filtered for internal QC)


title: RNA_Sample_13_left ovary_PRIMARY

description:
32761_0_l_ovary (Primary)
raw TPM column name: 32761_0_l_ovary


title: RNA_Sample_24_colon_RECURRENT2

description:
15815_1_colon (Recurrent)
raw TPM column name: N/A (filtered for internal QC)

value: Colon


title: L+DCI

status: Public on Aug 08 2023

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for tdTomato reporter and lentiviral BFP
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: iPSC-derived iAT2s grown in CKDCI medium in 3D

growth_protocol: SPC2B2 iPSCs were differentiated into iAT2 cells and either maintained in CKDCI medium, transduced with YAP5SA lentivirus, or grown in LDCI medium for 9 days.

extract_protocol:
Cells were dissociated to single cell using 0.05% trypsin and sorted for live cells using DRAQ7.
Single cells were captured for sequencing library preparation using a 10X Chromium (10X Genomics, Pleasanton, CA) instrument at the BUMC Single Cell Core. Single-cell RNA-seq libraries were prepared according to the Single Cell 3’ v2 Reagent Kits User Guide (10X Genomics). Sequence libraries were constructed using the Chromium Single-Cell 3’ Library Kit (10X Genomics). Sequencing libraries were loaded on a NextSeq500 (Illumina) to obtain a sequencing depth of~50K reads per cell. 623 iAT2s in CKDCI, 1212 cells from the YAP5SA in CKDCI condition and 1539 iAT1s in LDCI were captured and sequenced.

tag: media

value: L DCI

tag: lentivirus


title: CK+DCI

source_name: iPSC-derived iAT1s grown in LDCI medium in 3D

value: CK DCI


title: lib75294

status: Public on Aug 01 2023

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.
Supplementary files format and content: Supplementary_Table_1.csv: Table provides specific cell information from donors sorted from biopsies frozen live in DMSO/FCS.

source_name: Ulcerative Colitis

extract_protocol:
Immune cell populations were sorted from colon biopsies. SMARTseq v4 chemistry was used to generate cDNA following the manufacturer's instructions.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with paired-end 53-base reads and a target depth of 5 million reads per sample.

tag: donorid

value: gd T cells


title: lib75291


title: RNA_Sample_18_right ovary_PRIMARY

description:
19155_0_r_ovary (Primary)
raw TPM column name: N/A (filtered for internal QC)

value: Ovary right


title: lib75293


title: lib75279

source_name: Crohns Disease


title: lib75287


title: lib75290


title: lib75282


title: lib75288


title: lib75281


title: lib75289


title: lib75286


title: lib75273


title: lib75283


title: lib75280


title: lib75275


title: lib75285


title: lib75278


title: lib75274


title: lib75270


title: lib75272


title: lib75268


title: lib75284


title: lib75267


title: lib75269


title: lib75266


title: lib75271


title: lib75265


title: lib75264


title: lib75292


title: lib75277


title: lib75276


title: lib75259


title: lib75257


title: lib75261


title: lib75254


title: lib75253


title: lib75252


title: lib75251


title: lib75248


title: lib75263


title: lib75260


title: lib75258


title: lib75256


title: lib75244


title: lib75250


title: lib75249


title: lib75242


title: lib75262


title: lib75245


title: lib75239


title: lib75243


title: lib75246


title: lib75247


title: lib75238


title: lib75234

value: Memory CD4


title: lib75237


title: lib75235


title: lib75236


title: lib75241


title: lib75231


title: lib75233


title: lib75240


title: lib75230


title: lib75229


title: lib75232


title: lib75227


title: lib75226


title: lib75228


title: lib75225


title: lib75218


title: lib75221


title: lib75217


title: lib75219


title: lib75223


title: lib75224


title: lib75216


title: lib75220


title: lib75211


title: lib75208


title: lib75215


title: lib75214


title: lib75213


title: lib75222


title: lib75212


title: lib75210


title: lib75202


title: lib75199


title: lib75207


title: lib75209


title: lib75197


title: lib75196


title: lib75195


title: lib75193


title: lib75194


title: lib75192


title: lib75201


title: lib75203


title: lib75206


title: lib75189


title: lib75200


title: lib75198


title: lib75191


title: lib75204


title: lib75190


title: lib75188


title: lib75205


title: lib75185


title: lib75186


title: lib75184


title: lib75179


title: lib75180


title: lib75182


title: lib75181


title: lib75177


title: lib75174


title: lib75176


title: lib75173


title: lib75169


title: lib75187


title: lib75183


title: lib75164


title: lib75163

value: Memory CD8


title: lib75162


title: lib75161


title: lib75158


title: lib75160


title: lib75171


title: lib75170


title: lib75175


title: lib75166


title: lib75172


title: lib75155


title: lib75154


title: lib75178


title: lib75167


title: lib75159


title: lib75151


title: lib75157


title: lib75153


title: lib75156


title: lib75152


title: lib75165


title: lib75147


title: lib75146


title: lib75150


title: lib75143


title: lib75141


title: lib75145


title: lib75149


title: lib75142


title: lib75168


title: lib75148


title: lib75140


title: lib75138


title: lib75139


title: lib75137


title: lib75136


title: lib75133


title: lib75131


title: lib75127


title: lib75144


title: lib75132


title: lib75135


title: lib75125


title: lib75128


title: lib75123


title: lib75126


title: lib75134


title: lib75124


title: lib75130


title: lib75120


title: lib75122


title: lib75121


title: lib75129


title: lib75119


title: lib75118


title: lib75117


title: lib75114


title: lib75113


title: lib75115


title: lib75111


title: lib75112


title: lib75108


title: lib75116


title: lib75107


title: lib75106


title: lib75110


title: lib75105


title: lib75104


title: lib75109


title: lib75101


title: lib75100


title: lib75097


title: lib75098


title: lib75099


title: lib75094


title: lib75103


title: lib75255


title: lib75102


title: lib75095


title: lib75092


title: lib75093


title: lib75091


title: lib75089


title: lib75090


title: lib75088


title: lib75084


title: lib75083


title: lib75086


title: lib75085


title: lib75080


title: lib75087


title: lib75096


title: lib75081


title: lib75079


title: lib75082


title: lib75077


title: lib75078


title: lib75074


title: lib75073


title: lib75072


title: lib75075


title: lib75070


title: lib75069


title: lib75064


title: lib75071


title: lib75076


title: lib75067


title: lib75062


title: lib75065


title: lib75061


title: lib75063


title: lib75060


title: lib75068


title: lib75057


title: lib75056


title: lib75059


title: lib75055


title: lib75054


title: lib75053


title: lib75052


title: lib75049


title: lib75050


title: lib75066


title: lib75048


title: lib75051


title: lib75045


title: lib75042


title: lib75040


title: lib75038


title: lib75039


title: lib75037


title: lib75036


title: lib75033


title: lib75035


title: lib75031


title: lib75058


title: lib75030


title: lib75027


title: lib75046


title: lib75025


title: lib75024


title: lib75029


title: lib75022


title: lib75043


title: lib75041


title: lib75023


title: lib75020


title: lib75021


title: lib75028


title: lib75019


title: lib75032


title: lib75017


title: lib75018


title: lib75047


title: lib75044


title: lib75016


title: lib75014


title: lib75012


title: lib75034


title: lib75009


title: lib75008


title: lib75013


title: lib75015


title: lib75010


title: lib75026


title: lib75006


title: lib75005


title: lib75003


title: lib75004


title: lib75002


title: lib75000


title: lib74998


title: lib75001


title: lib74996


title: lib75011


title: lib74997


title: lib74994


title: lib74990


title: lib74992


title: lib74999


title: lib74989


title: lib74988


title: lib74991


title: lib74995


title: lib74987


title: lib74985


title: lib74993


title: lib74986


title: lib74983


title: lib74984


title: lib75007


title: lib74982


title: lib74981


title: lib74980


title: lib74978


title: lib74977


title: lib74979


title: lib74976


title: lib74975


title: lib74974


title: lib74973


title: lib74970


title: lib74972


title: lib74969


title: lib74971


title: lib74967


title: lib74965


title: lib74966


title: lib74963


title: lib74960


title: lib74958


title: lib74964


title: lib74959


title: lib74956


title: lib74957


title: lib74962


title: lib74952


title: lib74953


title: lib74955


title: lib74951


title: lib74949


title: IME

status: Public on May 01 2023

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

country: China

institute: Qilu Hospital

data_processing:
Illumina platform sequencing was used to obtain Raw off-machine sequences (Raw reads), and data interception was performed to obtain sequences to be analyzed (Clean reads). All subsequent analyses were based on Clean reads with GRCh38 V86 genome compilation as a reference and the corresponding GENCODE annotation file (version 25). The count matrix was screened, only protein-coding genes, long noncoding genes and antisense genes were retained, and the Ensembl ID was replaced with HGNC symbols.
Assembly: hg38
Supplementary files format and content: matrix files

source_name: PCNSL

extract_protocol:
The slides were inserted into the slide box, and the tissue sections were separated into separate reaction chambers. For prepermeability, the sections were incubated at 37°C with 0.5 U/mL collagenase (ThermoFisher) and 0.2 mg/mL BSA (ThermoFisher) for 20 min in HBSS buffer (ThermoFisher). The wells were washed with 0.1 x SSC (Sigma‒Aldrich), dissolved with 0.1% pepsin (Sigma‒Aldrich) in 0.1 m HCL (Sigma‒Aldrich) and permeated at 37°C for 10 min. After incubation, the pepsin solution was removed and washed with 0.1 x SSC.
After reverse transcription, Qubit3.0 was used for preliminary quantification, and the library was diluted to 1ng/ul. Then, Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, Q-PCR was performed using StepOnePlus Real-Time PCR System to accurately quantify the effective concentration of the library (the effective concentration of the library was required to be > 10nM) and ensure the quality of the library. Qualified libraries were sequenced using the Illumina platform.

value: PCNSL

value: Tumor


title: cold


title: IMS


title: hot


title: lib74968


title: FACS isolated VD Neurons [VDr81]

status: Public on Apr 06 2023

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

description: Library built using SoLo Ovation RNAseq kit from Tecan Genomics

data_processing:
Trimming TruSeq adapters using BBMap version 38.90, command bbduk, options ktrim=r k=23 mink=11 hdist=1 tpe tbo
Alignment using STAR version 2.7.7a, option --outFilterMatchNminOverLread 0.3
Deduplication based on Tecan SoLo Ovation UMIs, using umi-tools version 1.1.4, commands extract and dedup
Counting reads per gene using Subread version 2.0.3, command featureCounts
Assembly: Wormbase annotation WS289

organism: Caenorhabditis elegans

source_name: FACS C. elegans neurons

growth_protocol: Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22

extract_protocol:
Sorting protocol: Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™ III equipped with a 70-micron diameter nozzle. Cells were sorted into Trizol reagent LS
RNA was isolated using chloroform extraction
Libraries were prepared using Tecan SoLo Ovation RNAseq library

value: FACS isolated VD Neurons

value: untreated


title: FACS isolated VD Neurons [VDr78]


title: FACS isolated VD Neurons [VDr79]


title: lib74961


title: FACS isolated VC Neurons [VCr143]

value: FACS isolated VC Neurons


title: FACS isolated VD Neurons [VDr77]


title: FACS isolated VC Neurons [VCr140]


title: FACS isolated VC Neurons [VCr138]


title: FACS isolated VC Neurons [VCr142]


title: FACS isolated VB Neurons [VBr33]

value: FACS isolated VB Neurons


title: lib74954


title: FACS isolated VC Neurons [VCr139]


title: FACS isolated VB Neurons [VBr31]


title: FACS isolated VC Neurons [VCr141]


title: FACS isolated SMD Neurons [SMDr203]

value: FACS isolated SMD Neurons


title: FACS isolated SMD Neurons [SMDr201]


title: FACS isolated VB Neurons [VBr32]


title: FACS isolated VB Neurons [VBr34]


title: FACS isolated SMD Neurons [SMDr202]


title: FACS isolated SMD Neurons [SMDr200]


title: lib74950


title: FACS isolated SMB Neurons [SMBr199]

value: FACS isolated SMB Neurons


title: FACS isolated SMB Neurons [SMBr197]


title: FACS isolated SMB Neurons [SMBr196]


title: FACS isolated RMD Neurons [RMDr182]

value: FACS isolated RMD Neurons


title: FACS isolated SMB Neurons [SMBr195]


title: FACS isolated SMB Neurons [SMBr198]


title: FACS isolated RMD Neurons [RMDr181]


title: FACS isolated RMD Neurons [RMDr183]


title: FACS isolated RMD Neurons [RMDr179]


title: FACS isolated RIS Neurons [RISr131]

value: FACS isolated RIS Neurons


title: FACS isolated RMD Neurons [RMDr180]


title: FACS isolated RIS Neurons [RISr129]


title: FACS isolated RIM Neurons [RIMr225]

value: FACS isolated RIM Neurons


title: FACS isolated RIM Neurons [RIMr223]


title: FACS isolated RIM Neurons [RIMr224]


title: FACS isolated RIC Neurons [RICr135]

value: FACS isolated RIC Neurons


title: FACS isolated RIA Neurons [RIAr73]

value: FACS isolated RIA Neurons


title: FACS isolated RIS Neurons [RISr132]


title: FACS isolated RIA Neurons [RIAr71]


title: FACS isolated RIC Neurons [RICr134]


title: FACS isolated RIA Neurons [RIAr75]


title: FACS isolated RIC Neurons [RICr137]


title: FACS isolated RIM Neurons [RIMr222]


title: FACS isolated RIA Neurons [RIAr74]


title: FACS isolated RIC Neurons [RICr136]


title: FACS isolated RIA Neurons [RIAr72]


title: FACS isolated PVM Neurons [PVMr126]

value: FACS isolated PVM Neurons


title: FACS isolated PVM Neurons [PVMr123]


title: FACS isolated PVD Neurons [PVDr63]

value: FACS isolated PVD Neurons


title: FACS isolated PVC Neurons [PVCr218]

value: FACS isolated PVC Neurons


title: FACS isolated PVD Neurons [PVDr62]


title: FACS isolated PVC Neurons [PVCr216]


title: FACS isolated PHA Neurons [PHAr207]

value: FACS isolated PHA Neurons


title: FACS isolated PVC Neurons [PVCr214]


title: FACS isolated PVC Neurons [PVCr215]


title: FACS isolated PHA Neurons [PHAr206]


title: FACS isolated PHA Neurons [PHAr204]


title: FACS isolated OLQ Neurons [OLQr221]

value: FACS isolated OLQ Neurons


title: FACS isolated PHA Neurons [PHAr205]


title: FACS isolated OLQ Neurons [OLQr219]


title: FACS isolated OLQ Neurons [OLQr220]


title: FACS isolated OLL Neurons [OLLr213]

value: FACS isolated OLL Neurons


title: FACS isolated RIA Neurons [RIAr76]


title: FACS isolated NSM Neurons [NSMr69]

value: FACS isolated NSM Neurons


title: FACS isolated NSM Neurons [NSMr59]

value: untreated


title: FACS isolated OLL Neurons [OLLr212]


title: FACS isolated LUA Neurons [LUAr162]

value: FACS isolated LUA Neurons


title: FACS isolated LUA Neurons [LUAr160]


title: FACS isolated IL2 Neurons [IL2r97]

value: FACS isolated IL2 Neurons


title: FACS isolated LUA Neurons [LUAr163]


title: FACS isolated LUA Neurons [LUAr161]


title: FACS isolated IL1 Neurons [IL1r108]

value: FACS isolated IL1 Neurons


title: FACS isolated I5 Neurons [I5r210]

value: FACS isolated I5 Neurons


title: FACS isolated I5 Neurons [I5r211]


title: FACS isolated IL2 Neurons [IL2r94]


title: FACS isolated IL1 Neurons [IL1r105]


title: FACS isolated IL2 Neurons [IL2r95]


title: FACS isolated I5 Neurons [I5r208]


title: FACS isolated IL1 Neurons [IL1r106]


title: FACS isolated DVC Neurons [DVCr167]

value: FACS isolated DVC Neurons


title: FACS isolated I5 Neurons [I5r209]


title: FACS isolated DVC Neurons [DVCr166]


title: FACS isolated DD Neurons [DDr84]

value: FACS isolated DD Neurons


title: FACS isolated DD Neurons [DDr86]


title: FACS isolated DD Neurons [DDr83]


title: FACS isolated DD Neurons [DDr85]


title: FACS isolated DA Neurons [DAr89]

value: FACS isolated DA Neurons


title: FACS isolated NSM Neurons [NSMr68]


title: FACS isolated DA Neurons [DAr88]


title: FACS isolated IL2 Neurons [IL2r96]


title: FACS isolated DA Neurons [DAr87]


title: FACS isolated PVC Neurons [PVCr217]


title: FACS isolated CAN Neurons [CANr91]

value: FACS isolated CAN Neurons


title: FACS isolated DVC Neurons [DVCr165]


title: FACS isolated BAG Neurons [BAGr121]

value: FACS isolated BAG Neurons


title: FACS isolated DVC Neurons [DVCr164]


title: FACS isolated BAG Neurons [BAGr119]


title: FACS isolated AWC Neurons [AWCr157]

value: FACS isolated AWC Neurons


title: FACS isolated AWC Neurons [AWCr159]


title: FACS isolated AWB Neurons [AWBr54]

value: FACS isolated AWB Neurons


title: FACS isolated AWC Neurons [AWCr156]


title: FACS isolated AWB Neurons [AWBr52]


title: FACS isolated BAG Neurons [BAGr118]


title: FACS isolated AWC Neurons [AWCr158]


title: FACS isolated AWB Neurons [AWBr51]


title: FACS isolated DA Neurons [DAr90]


title: FACS isolated AWB Neurons [AWBr50]


title: FACS isolated AWA Neurons [AWAr20]

value: FACS isolated AWA Neurons


title: FACS isolated AWA Neurons [AWAr17]


title: FACS isolated AWA Neurons [AWAr18]


title: FACS isolated AWA Neurons [AWAr19]


title: FACS isolated CAN Neurons [CANr93]


title: FACS isolated AVM Neurons [AVMr226]

value: FACS isolated AVM Neurons


title: FACS isolated AVM Neurons [AVMr227]


title: FACS isolated AVL Neurons [AVLr232]

value: FACS isolated AVL Neurons


title: FACS isolated AVL Neurons [AVLr230]


title: FACS isolated BAG Neurons [BAGr120]


title: FACS isolated AVL Neurons [AVLr231]


title: FACS isolated AVK Neurons [AVKr111]

value: FACS isolated AVK Neurons


title: FACS isolated CAN Neurons [CANr104]


title: FACS isolated AVK Neurons [AVKr109]


title: FACS isolated AVK Neurons [AVKr112]


title: FACS isolated AVK Neurons [AVKr110]


title: FACS isolated AWB Neurons [AWBr53]


title: FACS isolated AVH Neurons [AVHr178]

value: FACS isolated AVH Neurons


title: FACS isolated AVH Neurons [AVHr176]

value: untreated


title: FACS isolated AVH Neurons [AVHr175]


title: FACS isolated AVG Neurons [AVGr43]

value: FACS isolated AVG Neurons


title: FACS isolated AVG Neurons [AVGr44]


title: FACS isolated AVE Neurons [AVEr40]

value: FACS isolated AVE Neurons


title: FACS isolated AVM Neurons [AVMr228]


title: FACS isolated AVE Neurons [AVEr42]


title: FACS isolated AVA Neurons [AVAr26]

value: FACS isolated AVA Neurons


title: FACS isolated AVG Neurons [AVGr45]


title: FACS isolated AVA Neurons [AVAr25]


title: FACS isolated AVA Neurons [AVAr23]


title: FACS isolated AVA Neurons [AVAr22]


title: FACS isolated AVA Neurons [AVAr24]


title: FACS isolated ASK Neurons [ASKr48]

value: FACS isolated ASK Neurons


title: FACS isolated ASK Neurons [ASKr49]


title: FACS isolated AVA Neurons [AVAr21]


title: FACS isolated ASK Neurons [ASKr46]


title: FACS isolated ASK Neurons [ASKr47]


title: FACS isolated ASI Neurons [ASIr154]

value: FACS isolated ASI Neurons


title: FACS isolated ASI Neurons [ASIr152]


title: FACS isolated AVH Neurons [AVHr177]


title: FACS isolated ASI Neurons [ASIr155]


title: FACS isolated ASI Neurons [ASIr153]


title: FACS isolated ASG Neurons [ASGr15]

value: FACS isolated ASG Neurons


title: FACS isolated ASG Neurons [ASGr16]


title: FACS isolated ASG Neurons [ASGr14]


title: FACS isolated ASER Neurons [ASERr147]

value: FACS isolated ASER Neurons


title: FACS isolated ASG Neurons [ASGr13]


title: FACS isolated ASEL Neurons [ASELr150]

value: FACS isolated ASEL Neurons


title: FACS isolated ASER Neurons [ASERr146]


title: FACS isolated AVE Neurons [AVEr41]


title: FACS isolated AIN Neurons [AINr189]

value: FACS isolated AIN Neurons


title: FACS isolated AIY Neurons [AIYr67]

value: FACS isolated AIY Neurons


title: FACS isolated ASER Neurons [ASERr145]


title: FACS isolated ASEL Neurons [ASELr149]


title: FACS isolated AIY Neurons [AIYr65]


title: FACS isolated AIN Neurons [AINr188]


title: FACS isolated AIY Neurons [AIYr66]


title: FACS isolated AIN Neurons [AINr187]


title: FACS isolated ASER Neurons [ASERr144]


title: FACS isolated AIM Neurons [AIMr193]

value: FACS isolated AIM Neurons


title: FACS isolated AIN Neurons [AINr185]


title: FACS isolated AIM Neurons [AIMr191]


title: FACS isolated AIM Neurons [AIMr190]


title: FACS isolated AFD Neurons [AFDr38]

value: FACS isolated AFD Neurons


title: FACS isolated AIM Neurons [AIMr192]


title: FACS isolated AIN Neurons [AINr184]


title: FACS isolated AFD Neurons [AFDr39]


title: FACS isolated AFD Neurons [AFDr37]


title: FACS isolated AIN Neurons [AINr186]


title: FACS isolated ADL Neurons [ADLr174]

value: FACS isolated ADL Neurons


title: FACS isolated AFD Neurons [AFDr36]


title: FACS isolated ADL Neurons [ADLr173]


title: FACS isolated AFD Neurons [AFDr35]


title: FACS isolated ASEL Neurons [ASELr151]


title: FACS isolated ADL Neurons [ADLr172]


title: FACS isolated ADL Neurons [ADLr171]


title: BSCHF_942

status: Public on Mar 01 2023

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: human whole blood RNA profile

hyb_protocol: 5 μg of fragmented, end–labelled sense strand target cDNA was hybridized to each array and scanned using a Gene Chip Scanner 30007G

scan_protocol: standard protocol

data_processing: The normalisation used the method by Welsh et al called IRON. BMC Bioinformatics. 2013 May 7;14:153. doi: 10.1186/1471-2105-14-153.

label: biotin

source_name: whole blood

label_protocol: The RNA was processed to single-stranded sense fragmented DNA using the GeneChip® WT PLUS Reagent Kit which relies on a reverse transcription priming strategy that primes both poly-A and non-poly-A RNA

extract_protocol: PAXgene tubes (Qiagen) and RNA was isolated using TRizol® (Life Technologies) and dissolved in 20 μl RNAse-free water.

value: whole blood

tag: diagnosis

value: Chronic Heart Failure (CHF)

value: Male


title: BSCHF_935

description: human whole blood RNA profile

value: Female


title: BSCHF_943

description: human whole blood RNA profile


title: BSCHF_922

description: human whole blood RNA profile


title: BSCHF_939

description: human whole blood RNA profile


title: BSCHF_938

description: human whole blood RNA profile


title: BSCHF_919

description: human whole blood RNA profile


title: BSCHF_917

description: human whole blood RNA profile


title: BSCHF_940

description: human whole blood RNA profile


title: BSCHF_934

description: human whole blood RNA profile


title: BSCHF_931

description: human whole blood RNA profile


title: BSCHF_937

description: human whole blood RNA profile


title: BSCHF_936

description: human whole blood RNA profile


title: BSCHF_929

description: human whole blood RNA profile


title: BSCHF_941

description: human whole blood RNA profile


title: BSCHF_921

description: human whole blood RNA profile


title: BSCHF_932

description: human whole blood RNA profile


title: BSCHF_933

description: human whole blood RNA profile


title: BSCHF_930

description: human whole blood RNA profile


title: BSCHF_926

description: human whole blood RNA profile


title: BSCHF_927

description: human whole blood RNA profile


title: BSCHF_928

description: human whole blood RNA profile


title: BSCHF_920

description: human whole blood RNA profile


title: BSCHF_944

description: human whole blood RNA profile


title: BSCHF_924

description: human whole blood RNA profile


title: BSCHF_923

description: human whole blood RNA profile


title: BSCHF_918

description: human whole blood RNA profile


title: BSCHF_925

description: human whole blood RNA profile


title: BSCHF_916

description: human whole blood RNA profile


title: BSCHF_911

description: human whole blood RNA profile


title: BSCHF_914

description: human whole blood RNA profile


title: BSCHF_907

description: human whole blood RNA profile


title: BSCHF_910

description: human whole blood RNA profile


title: BSCHF_901

description: human whole blood RNA profile


title: BSCHF_908

description: human whole blood RNA profile


title: BSCHF_909

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